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Literature summary for extracted from

  • Hsu, C.; West, A.H.; Cook, P.F.
    Evidence for an induced conformational change in the catalytic mechanism of homoisocitrate dehydrogenase for Saccharomyces cerevisiae: Characterization of the D271N mutant enzyme (2015), Arch. Biochem. Biophys., 584, 20-27.
    View publication on PubMedView publication on EuropePMC


Cloned (Comment) Organism
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Saccharomyces cerevisiae


Protein Variants Comment Organism
D271N site-directed mutagenesis, mutation of a metal ion ligand and binding determinant for Mg2+, to N. The mutant enzyme shows a decrease of 520fold in V and V/Km_Mg2+, suggesting that the same step(s) limit the reaction at limiting and saturating MgHIc concentrations Saccharomyces cerevisiae
K206M site-directed mutagenesis, inactive mutant Saccharomyces cerevisiae
Y150F site-directed mutagenesis, inactive mutant Saccharomyces cerevisiae


Inhibitors Comment Organism Structure
3-acetylpyridine adenine dinucleotide 3'-phosphate 3-AcPyrADP, competitive versus NAD+ Saccharomyces cerevisiae
thiahomoisocitrate competitive versus homoisocitrate Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
additional information Michaelis-Menten kinetics, the enzyme shows a steady-state random kinetic mechanism with a preferred order of addition of Mg2+ prior to NAD+. The same step(s) limit the reaction at limiting and saturating Mg2+ concentrations. Solvent kinetic deuterium isotope effects and viscosity effects are consistent with a rate-limiting pre-catalytic conformational change at saturating reactant concentrations Saccharomyces cerevisiae


Metals/Ions Comment Organism Structure
K+ the enzyme requires a potassium ion as an activator, for optimal binding of NAD+ Saccharomyces cerevisiae
Mg2+ required, three conserved aspartate residues, D243, D267 and D271, coordinate Mg2+, which is also coordinated to the alpha-carboxylate and alpha-hydroxyl of homoisocitrate Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
homoisocitrate + NAD+ Saccharomyces cerevisiae
2-oxoadipate + CO2 + NADH + H+


Organism UniProt Comment Textmining
Saccharomyces cerevisiae P40495

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chrmatography Saccharomyces cerevisiae


Reaction Comment Organism Reaction ID
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+ there are 2 groups acting as acid-base catalysts in the reaction. One residue with a pKa of 6.5-7.0 serves as the general base to accept a proton as the beta-hydroxy acid is oxidized to the beta-keto acid, and this residue participates in all three of the chemical steps, acting to shuttle a proton between the C2 hydroxyl and itself. The metal ion then acts as a Lewis acid to catalyze the decarboxylation of the beta-ketoacid, with the general base donating a proton to the keto oxygen as the enol of alpha-ketoadipate is formed. A second residue with a pKa of 9.5 likely catalyzes the tautomerization step by donating a proton to the enol to give the final product. Catalytic rapid equilibrium random kinetic mechanism, overview Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
homoisocitrate + NAD+
Saccharomyces cerevisiae 2-oxoadipate + CO2 + NADH + H+
additional information the wild-type enzyme with isocitrate as the substrate is about 200times slower than with homoisocitrate Saccharomyces cerevisiae ?


Synonyms Comment Organism
3-carboxy-2-hydroxyadipate dehydrogenase
Saccharomyces cerevisiae
Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
assay at Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
5.5 9.5 pH independence of the catalytic reaction over the range of pH 5.5-9.5 Saccharomyces cerevisiae

pH Range

pH Minimum pH Maximum Comment Organism
5.5 9.5 pH independence of the catalytic reaction over the range of pH 5.5-9.5, pH profiles Saccharomyces cerevisiae


Cofactor Comment Organism Structure
Saccharomyces cerevisiae
Saccharomyces cerevisiae

General Information

General Information Comment Organism
evolution the enzyme is a member of the family of pyridine dinucleotide-dependent beta-hydroxyacid oxidative decarboxylating dehydrogenases, specifically the family that has (R)-beta-hydroxyacid substrates, including isocitrate dehydrogenase (ICDH) among others. Superposition of available structures of the malic enzyme, isopropylmalate dehydrogenase, IcDH, and HIcDH show a similar overall geometry of residues in the substrate and metal ion binding sites. A Lys (general base)-Tyr (general acid) pair is conserved among these enzymes. The similar structural geometry in the active site suggests a similar general chemical mechanism. Three aspartate residues are conserved in the active sites of all HIcDHs sequenced to data, and are also conserved across the family of pyridine nucleotide-dependent oxidative decarboxylases including malic enzyme Saccharomyces cerevisiae
metabolism homoisocitrate dehydrogenase catalyzes the fourth step of the alpha-aminadipate pathway, the NAD+-dependent conversion of homoisocitrate to alpha-ketoadipate Saccharomyces cerevisiae
additional information a conformational change to close the active site and organize the active site for catalysis contributes to rate limitation of the overall reaction of the Saccharomyces cerevisiae enzyme HIcDH. Residues K206 and Y150 of ScHIcDH are a Lys-Tyr pair in the active site acting as the general base and general acid in the reaction. A slow conformational change is required to close the site upon the binding of MgHIc prior to catalysis. With the slow substrate isocitrate, hydride transfer and decarboxylation steps contribute to rate limitation, and the decarboxylation step is the slower of the two Saccharomyces cerevisiae